fix

docs/README.md

@@ -8,21 +8,23 @@
 
 _ZARP_ is a [Snakemake][snakemake] workflow ...
 
-TODO: Complete intro/summary section
+**TODO:** Complete intro/summary section
 
-NOTE: Include references in `/includes/references.md`
-NOTE: Include abbreviations in `includes/abbreviations.md` (example: EAWNKWIMPR)
-NOTE: Include emojis (example: :rocket:)
-NOTE: Check out the [ZARP-cli docs pages](https://zavolab.github.io/zarp-cli/)
+**NOTES TO SELF:**
+
+- Include references in `/includes/references.md`
+- Include abbreviations in `includes/abbreviations.md` (example: EAWNKWIMPR)
+- Include emojis (example: :rocket:)
+- Check out the [ZARP-cli docs pages](https://zavolab.github.io/zarp-cli/)
 for inspiration.
-NOTE: Check out [MKDocs](https://www.mkdocs.org/) and [Material for
+- Check out [MKDocs](https://www.mkdocs.org/) and [Material for
 MkDocs](https://squidfunk.github.io/mkdocs-material/) docs for more info
 
 ## How does it work?
 
 Briefly, when a _ZARP_ run is triggered, ...
 
-TODO: Complete section
+**TODO:** Complete section
 
 ## How to cite
 
@@ -48,8 +50,8 @@ Coming soon...
 
 There are several ways to get in touch with us:
 
-- For ZARP usage questions, please use the [_ZARP_ Q&A forum][zarp-qa]  
-  (requires [GitHub registration][github-signup])
+- For ZARP usage questions, please use the [_ZARP_ Q&A forum][zarp-qa] (requires
+  [GitHub registration][github-signup])
 - For feature suggestions and bug reports, please use either the
   [ZARP][zarp-issue-tracker] or [ZARP-cli][zarp-cli-issue-tracker] issue
   tracker (requires [GitHub registration][github-signup])

docs/guides/installation.md

@@ -10,13 +10,12 @@ Installation requires the following:
 - [Conda][conda] (tested with `conda 22.11.1`)
 - [Mamba][mamba] (tested with `mamba 1.3.0`)
 - [Singularity][singularity] (tested with `singularity 3.8.6`; not required
-  if you have root permissions on the machine you would like to install
-  _ZARP-cli_ on; in that case choose one of the `.root.` environment file
-  flavors [below](#3-install-app-dependencies))
+  if you have root permissions on the machine you would like to install _ZARP_
+  on; in that case, see [below](#2-set-up-conda-environment))
 
 > Other versions, especially older ones, are not guaranteed to work.
 
-TODO: Add/replace requirements/versions
+**TODO:** Add/replace requirements/versions and check that everything is correct
 
 ## Installation steps
 
@@ -29,4 +28,6 @@ git clone git@github.com:zavolanlab/zarp
 # or: git clone https://github.com/zavolanlab/zarp.git
 ```
 
-TODO: Add on...
+### 2. Set up Conda environment
+
+**TODO:** Add on...